D-2-deoxyribose and D-arabinose, but not D-ribose, stabilize the cytosine tetrad (i-DNA) structure

Journal of Biomolecular Structure & Dynamics
S Robidoux, M J Damha

Abstract

Described here are studies exploring the effect of the sugar-phosphate backbone on the stability of i-tetrads in solution [K. Gehring et al. Nature 363, 561-565 (1993)]. In the accompanying paper, branched oligonucleotides are shown to be effective probes for organizing oligodeoxycytidine strands into I-motif structures (C-tetrads). Specifically, the joining of a pair of parallel deoxycytidylate strands with a riboadenosine "linker" leads to marked enhancement in stability of the tetrad structure. To further characterize the nature of the sugar-sugar interactions in this novel structure, branched oligonucleotides containing D-arabinocytidine and D-ribocytidine were synthesized and their association properties examined. The ribo oligomers were prepared in two regioisomeric forms differing only in the connectivities of the deoxycytidine strands, i.e., 3'-to-5' versus 2'-to-5' linked dC5 strands. The branched D-deoxycytidine analogue, rA(2',5'-dC5)3',5'-dC5, which previously has been shown to fold into a bimolecular I-motif, served as model system. It is found that the arabinose substitution leads to hypochromic structures that are characteristic of four-stranded intercalated DNA and has little, if any, effect on the stability of ...Continue Reading

References

Apr 11, 1992·Nucleic Acids Research·R KierzekD H Turner
Feb 1, 1983·Proceedings of the National Academy of Sciences of the United States of America·J C Wallace, M Edmonds
Apr 25, 1995·Proceedings of the National Academy of Sciences of the United States of America·C KangA Rich
Nov 22, 1994·Biochemistry·L ChenA Rich
Nov 22, 1994·Proceedings of the National Academy of Sciences of the United States of America·C H KangA Rich
Nov 15, 1993·Proceedings of the National Academy of Sciences of the United States of America·R JinK J Breslauer
Oct 29, 1996·Proceedings of the National Academy of Sciences of the United States of America·I BergerA Rich
Jan 24, 1998·Journal of Biomolecular Structure & Dynamics·S RobidouxM J Damha
May 25, 1963·Nature·R LANGRIDGE, A RICH
Mar 1, 1963·Biochemistry·E O AKINRIMISIP O TS'O

❮ Previous
Next ❯

Citations

Jun 14, 2000·Current Opinion in Structural Biology·M Guéron, J L Leroy
May 12, 2016·Nucleic Acids Research·Hala Abou AssiMasad J Damha
Aug 9, 2001·Journal of Molecular Biology·K SnoussiJ L Leroy
Apr 14, 2017·Chembiochem : a European Journal of Chemical Biology·Anna AviñóRamon Eritja
Nov 22, 2005·Angewandte Chemie·John A BrazierRichard Cosstick
Feb 24, 2018·Nucleic Acids Research·Vladimir B TsvetkovAndrey V Aralov
Jun 22, 2018·Organic & Biomolecular Chemistry·Yawei SunDongsheng Liu
Jul 26, 2008·Chemical Communications : Chem Comm·Clare P FennaJulie Fisher
Nov 3, 2017·Chemistry : a European Journal·Hala Abou AssiMasad J Damha
Aug 21, 2018·Nucleic Acids Research·Hala Abou AssiMasad J Damha
Aug 7, 2020·Organic & Biomolecular Chemistry·Alexandre DevauxEric Defrancq
Mar 2, 2021·Chemical Society Reviews·Luke K McKenzieMarcel Hollenstein

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.